Is Color alignments by base modification (5mC) supported by igv.js?

[yaarau]

Hello,
I'd like to set my igv.js application to color the alignments by base modification (5mC). Is this possible? If so, can you please direct me to documentation how to do this? thank you!

[jrobinso]

Not yet.

[yaarau]

Thank you.
Is it expected to be implemented soon? If so, can you please estimate when? thanks again

[jrobinso]

Sorry, I'm working on it but can't give you a time estimate.

[jrobinso]

This is supported now in the main branch, it will be included in the upcoming release. Below is a session illustrating some options for a dataset with 5mC and 6mA modifications.

{
  "genome": "hg38",
  "locus": "chr11:119094729-119094804",
  "tracks": [
    {
      "type": "alignment",
      "format": "bam",
      "url":      "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam",
      "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam.bai",
      "height": 300,
      "name": "Base modifications",
      "colorBy": "basemod",
      "groupBy": "strand"
    },
    {
      "type": "alignment",
      "format": "bam",
      "url":      "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam",
      "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam.bai",
      "height": 300,
      "name": "Base modifications - 2 Color",
      "colorBy": "basemod2",
      "groupBy": "strand",
      "baseModificationThreshold": 0
    },
    {
      "type": "alignment",
      "format": "bam",
      "url":      "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam",
      "indexURL": "https://igv-genepattern-org.s3.amazonaws.com/test/baseMods/6mA/pacbio/HG002_chr11_119076212_119102218.bam.bai",
      "height": 300,
      "name": "5mC modifications - 2 Color",
      "colorBy": "basemod2:m",
      "groupBy": "strand",
      "baseModificationThreshold": 0
    }
  ]
}